


Hydra Born Connection

by Siri_Tachi



Category: Marvel Cinematic Universe
Genre: Aftermath of Torture, Angst, Depression, F/M, Fluff, Fluff and Angst, Gen, Pregnancy, References to Depression, Torture, Whump
Language: English
Status: Completed
Published: 2020-02-25
Updated: 2020-02-27
Packaged: 2021-02-28 04:54:05
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 18
Words: 11,985
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/22898332
Author URL: https://archiveofourown.org/users/Siri_Tachi/pseuds/Siri_Tachi
Summary: Mature: This story is rated mature for depictions of violence.TW: There will be torture and panic attacks so if that triggers you, use caution if you continue reading this.Aunt May recently moved to Florida for her job, but not wanting to uproot her nephew, Peter Parker is now living with Tony Stark in the Avengers Tower. But when Spiderman and Iron Man go on patrol together it takes a turn for the worse. Stark is gone.Check out the sequel: What Blood Is Used ForI OWN NOTHING EXCEPT THE PLOT OF THIS STORY AND ANY ORIGINAL CHARACTERS.
Relationships: Pepper Potts & Tony Stark, Pepper Potts/Tony Stark
Kudos: 2





	1. Chapter 1

"Wait-seriously?" Peter asked excitedly. Tony had just suggested that he could come along this Friday with Peter, while he patrolled. Usually Tony would only come along on patrol when it was Peter's birthday. Even then, it would take some convincing.

"Sure, why not?" Tony replied, "I mean, we don't have to though-"

"N-no! " Peter cut off, "It's just that, normally you only come along when it's my birthday or something, and even then you're pretty hesitant-"

"Kid," interrupted Tony.

" Right, s-sorry. I just... Wow," breathed Peter, a huge grin on his face, "this is awesome, I can't wait! Thank you Mr. Stark." Peter said as he hugged his mentor.

Tony chuckled, "Anything for you kid." He hugged Peter tightly, but noticed him wince and loosened his grip a little. Peter eventually pulled away from the hug. "Oh man, wait 'till I tell Ned about this. He's gonna be so excited!" Peter ran off to his room in the tower, where he's been staying while Aunt May was on vacation. He brought out his phone and called Ned. The phone started to ring as he flipped onto his bed. "Pick up, pick up, pick-"

"Peter?" Ned asked.

"Ned! Oh my gosh you won't believe what just happened. "

"Well it would have to have been something pretty big. You were in a crummy mood after the incident with Flash today. Speaking of which, how's your side?"

"Oh yeah, I had forgotten about that..." Peter recalled what had happened right after lunch that day. Him and Ned had been walking to Peter's locker so he could drop off some books. Flash had come running up from behind them and ran straight in-between the two. Elbowing Peter hard on his right side, causing him to slam into the lockers, hitting his head. 

"I still have a bad headache, but my side isn't throbbing anymore, it only hurts to touch." responded Peter, gingerly touching his side and wincing as he did so. "Anyways, back to why I called."

"Oh yeah, what were you going to say?" inquired Ned.

"Me and Mr. Stark are going on patrol together this Friday!" Exclaimed Peter, unable to contain his excitement.

Ned was shocked. "No. Freaking. Way. Are you actually?"

"Yeah man. And get this, Mr. Stark was the one to suggest it."

" This-this is so cool, dude. You have to tell me how it goes, what all happens."

" I will, I promise." laughed Peter. "Bye Ned."

"Bye Peter." Ned hung up.

~~~~~~~~~~~~

They knew they couldn't just kidnap Peter outright. No, Stark would undoubtedly find him in no time. They would have to make the kid come on his own accord. That's why they'd take Iron Man himself.

~~~~~~~~~~~~


	2. Chapter 2

When Peter woke up Friday morning, nothing could get him down. Not even his multiple encounters with Flash, or when he got the wrong answer to a question his chemistry teacher asked. Usually when that'd happen, it would really lower his self-esteem. But not today. Because today, Spiderman and Iron Man would be going on patrol, together. 

~~~~~~~~~~~~

When Peter got back to the Tower after school that day, he tossed his backpack onto the couch before heading to the kitchen. "Hey Fri, where's Tony?" He asked wile rummaging through the fridge.

"Boss is at an SI meeting with Ms. Potts. He is expected to arrive home at 5p.m." replied Friday, Tony's AI.

"Thanks Fri." Peter pulled out some leftover pizza from the other night and placed it inside the microwave. 

"Of course, Peter." The AI said before going silent. 

"That gives me one hour," Peter thought to himself, "that's plenty of time to eat pizza and make some more web fluid." Peter hopped up on a bar stool at the island and began eating. Halfway through his food, Natasha came in and poured herself a cup of coffee.

"Hi Miss Romanoff." Peter said cheerfully.

"Hello Peter," Natasha replied warmly, "and please, like I've said many times before, call me Natasha."

Peter blushed. "O-oh, sorry Miss Ro- I mean Natasha."

Natasha chuckled at the kid. She definitely had a soft spot in her heart for Peter, as she knew most of, if not all the Avengers did. "How was school today?" She sipped her coffee.

"Well, pretty good, except for the usual run-ins with Flash and the fact that I answered a question wrongly in chemistry class. I'm not even sure why, it was a fairly simple question. My mind has just been elsewhere today." Peter recounted.

"Aw, I hate to hear that Peter. I'm surprised you're in such a good mood after all that." mused Natasha.

"Normally I wouldn't be, but today is the day Mr. Stark and I are going on a patrol together." beamed Peter, finished with his pizza.

Natasha smiled gently, "That sounds like a lot of fun."

"I hope so. Now that I'm thinking about it, I really should go make some more web fluid for tonight." Peter stood up and placed his plate in the dishwasher. "Will I see you later, Natasha?"

"Of course, I just finished a mission yesterday, so I'll be resting here a while." assured Natasha.

"Awesome! See you later then." Peter bounced off to the lab Mr. Stark had given him, waving to Bruce along the way.

Natasha smiled at the boy's retreating figure. "So young, so pure," she thought. "Never change Peter," she said quietly.

"Never change."

~~~~~~~~~~~~

Peter was so focused on his web fluid he didn't even notice it was five o'clock until Friday told him.

"Sir," she said, "it is currently 5:03 p.m. and Boss has arrived home."

"Five o'clock already? Wow. " He thought. "Thanks Friday." He said aloud. 

"Of course, Peter."

Peter hurried out of his lab and rode the elevator up to the main floor. When he stepped out, he immediately saw Mr. Stark, who was sitting on the couch. Peter went over to him and sat down. 

"Hey kid," greeted Tony.

"Hi Mr. Stark! So like, I know we can't head out till after supper, when it's dark. That's brings me to a question what's for supper? Who's all joining us? Oh, and what was your meeting about?" rambled Peter

"Whoa kid," Tony said, holding up a hand to quiet him. "You're going to give me a headache," he teased. "A) I was thinking spaghetti. B) Natasha, Rhodey, Bruce and Steve, I think. And lastly, just boring company stuff."

"Okay," smiled Peter. He was so full of energy that he could've started bouncing off the walls (quite literally, being that he was Spiderman), but he tried to restating himself. 

"How was school?" asked Tony.

Peter recounted everything that had happened, all the way up to where they were now.

"That Flash kid is still bullying you that much? Are you sure you don't want me to say something to him?" Mr. Stark asked worriedly.

"Y-yeah, I'm sure. Really, it's nothing Mr. Stark. I can handle it." Peter replied.

Tony still looked doubtful, but after a few seconds of staring at Peter, he stood. "Let's go make dinner shall we?"

~~~~~~~~~~~~

Almost ready to begin.

Stark and the kid will soon be ours.

~~~~~~~~~~~~


	3. Chapter 3

After dinner, around 7 p.m., they had their suits on and were ready to leave. "Ready Underoos?" Tony asked.

"Definitely Mr. Stark." Peter replied while pulling on his mask.

"Then let's go," Tony flew off the Tower's balcony and Peter followed closely, swinging on his webs.

"So kid where do you usually go?"

"I go everywhere Mr. Stark, wherever Karen tells me there's crime." Peter replied.

"Speaking of which," Karen cut in, "3 blocks to your left a woman and her child are being mugged. 

"That's us, Mr. Stark." Peter made a sharp left turn, as did Tony. They quickly spotted the attacker, Tony hanging back and letting Spiderman handle this one.

Peter quickly landed in between the mugged and his victims. "Didn't anyone ever tell you not to take stuff that doesn't belong to you?" Spiderman asked while webbing the guy up. When he was finished he swung up to the rooftop where Mr. Stark was waiting.

"Good job kid." Mr. Stark commented while walking up to him.

"Thanks Mr. Stark, we should probably get going though." Peter hopped off the roof and swung down the street.

For the next 4 1/2 hours, Peter and Tony swung and flew across Queens, going wherever Karen told them they were needed. They were sitting on a rooftop, feet dangling off the edge, eating churros that an old lady has bought for them. "Almost midnight kiddo, we should probably head back." 

Peter sighed, "Yeah, I guess you're right." They had just stood up and see about to jump off the roof when Peter gasped. He lunged toward Tony as a weirdly glowing knife flew at him. Fortunately, Peter was able to push Tony out of the molten knife's way. Unfortunately, however, he couldn't leap out of its way and it hit his left bicep, slicing it deeply. He cried out in pain, grasping his arm and falling to his knees. "It burns," he thought, removing his hand to see it pouring out blood, "that knife was red hot, why is it still bleeding? It should be cauterized. This is probably some alien tech still around from Toomes. Gosh do I hate space."

"Pete!" Tony stood in front of him protectively, repulsors ready to fire. "Show yourself! Who did this?" He turned in a circle, looking for who hurt his kid. That was the wrong thing to do. While his back was turned the guy shot Stark with a powerful EMP (electromagnetic pulse), short-circuiting his Iron Man suit and electrocuting him. He crashed to the ground beside Peter.

The shooter slowly walked out of the shadows and towards the fallen two. Peter struggled to his feet, his arm still heavily bleeding. "W-who are you? What do you want?"

The shooter laughed cruelly, the sound slightly muffled by a mask that concealed his nose and mouth. His vivid blue eyes gleamed coldly, "I'm a bad guy," he snarled, "and I want you."

Peter's eyes widened as the thrusters for a jetpack fired up on the guys back. Spiderman jumped out of the way, but soon learned Evil Dude wasn't trying to kidnap him. Evil Dude grabbed the still limp body of Iron Man and flew off into the starless, black sky.

Peter tried in vain to shoot his webs and bring them back. When he couldn't see them any longer, the tears finally started to fall. Clutching his arm he leaned against the ledge of the roof crying. "I failed you," he sobbed, "I failed you Mr. Stark, I'm so sorry." Peter sat crying and bleeding, not having the will to move.

~~~~~~~~~~~~


	4. Chapter 4

When Tony woke up he was sitting on a wooden chair in a small and grey concrete room. He was wearing a black t-shirt and grey sweatpants. His wrists and ankles were cuffed together by thick metal bands, which had chains connecting to the floor. "Where am I?" Tony thought. The last thing he remembered was standing over his hurt kid. Oh gosh, Peter. What happened while he was out? Is Peter still alive? His thoughts were cut short by someone entering the room. 

"Amazing, you woke up quicker than expected." The man was wearing a mask that covered his nose and mouth. Probably a precaution so if he ever escaped he couldn't give a facial description. Tony realized the man was still talking and pulled himself from his thoughts. "...better for us I suppose. Where is it?"

"Where is what?" He was confused, what could this guy possibly want that he had on him. 

"Don't play stupid," the man sneered, "what does everyone who kidnaps people want to know? Where's your tracker implant?"

Tony tried to played dumb, "My what? I don't have a tracker in me."

"It's ok. If you won't willingly tell us, we have a way that might work." The man clicked a button on a remote in his hand and a television screen lit up in the corner. It looked like live feed, but if that was true, Stark was still somewhere in New York City or it's outskirts. The screen showed Spiderman struggling to his feet, while pulling his mask over his tear stained face. Not good, now they know who he is. But the worst part was when Spiderman turned to shoot his webs and swing home, there was a targeting laser from a sniper's gun trained on his back, right behind his heart. 

"Tell us where the tracker is and your precious intern won't get shot." said the man as he pulled out a knife. Tony watched, distressed, as the targeting laser stayed on his back, following him, as he stumbled to get back to the tower. Then a gun fired. 

"NO!" Tony yelled. He quickly realized, much to his relief, that it was just a warning shot and it didn't actually hit Peter. Peter however, did yank around, startled, searching for where it came from. While he was distracted, Spiderman smacked into the side of a building. Thankfully he didn't fall, sticking to the wall by his fingertips. 

"Fine. I'll tell you, but only when Peter gets back to the tower-"

Another shot rang out, this time, hitting an inch above Spiderman's head. "I think you'll tell us now."

Tony stared at the man, "How can I be certain that as soon as I tell you, you won't just kill him?"

"Trust me. We'd much rather have him alive, makes this whole experimentation process simpler."

Tony's eyes widened in fear, he couldn't let these freaks experiment on his kid. He didn't want him dead though, either. Stark would just have to trust that the other avengers could protect Peter from whoever these people were. He sighed, staring at the television screen, "left forearm, right below the elbow."

The man grinned delightedly and grabbed Tony's arm violently. He took his knife and started to carve Stark's skin where he said the tracker was. Tony gasped in pain, not daring to look at his arm. This man was certainly not being gentle.

What felt like an eternity later but what was in reality, seven minutes, the man pulled out a tiny piece of technology. He held it triumphantly in front of him. "That wasn't too hard." the man said as he crushed the tracker in his fingers, before walking out of the room. For the first time, Tony looked at his arm and almost fainted at the sight. A huge section of it was torn and mangled and slightly swollen, not to mention that it was profusely bleeding. "Not good." He thought, forcing himself to look away. He knew he needed to stop the bleeding but, with his hands cuffed, that was simply impossible. So he turned his thoughts to the crushing reality that with his tracker destroyed, no one would be able to find him. Just great.

~~~~~~~~~~~~


	5. Chapter 5

Natasha woke from her nightmare with a start. "What is wrong with me?" she thought, "That was third time this week." She swung her legs over the side of her bed and stood, grabbing her robe. Natasha went to the kitchen. As she was grabbing a water glass, she saw someone drop onto the balcony right in front of the glass door. In the low lighting she couldn't make out who it was. The person had fallen to his knees, and used his right hand to knock on the door, before resting it there. Her eyes widened when she saw the bloody handprints he had left. 

"Friday," she whispered, "turn on the living room and balcony lights."

Natasha was horrified to see that it was Spiderman. She rushed forward and knelt, sliding the door open. She gently pulled his mask off to see his tear stained face. "Peter..." Natasha said quietly, "What, what happened. Where's Tony?"

At the mention of Tony's name, fresh tears started to fall and he leaned into Natasha, burying his face in her shoulder. If it was anyone else, she would have immediately recoiled, but this was Peter. Natasha rubbed his back in an attempt to soothe him. She really wasn't quite sure what to do, she had never been good at the touchy feely part of people. Thankfully, Steve walked into the room at that moment. She didn't think they had made that much noise, but he always had been a light sleeper.

"Natasha? What's going-oh my gosh, what's wrong with his arm?" 

Natasha looked at Steve, "His, what?" 

Steve knelt beside her and gently grabbed Peter's left arm. "Look, he has a huge cut."

"Oh my gosh, how did I not notice that." Natasha gaped at the wound. "Friday, tell Bruce to get to the med bay. Steve, can you carry him?"

"Of course," he replied, gently lifting Peter and carrying him down to the med bay and laying him on a table. Barely a minute after they got there, Bruce stumbled in. He was wearing gray sweatpants and a dark blue t-shirt. His hair was disheveled from just waking up. Bruce looked at Natasha, "What's happening?"

She pointed to Peter, "He just landed on the balcony, alone, about 10 minutes ago. His arm's badly cut."

Bruce went over and bent down to get a closer look at Peter's arm. "Yeah, it is. He needs stitches, but because of his enhanced metabolism, any pain killers I give him will wear off too quickly. You'll have to hold him down."

Steve and Natasha exchanged a glance. They had both trained with the kid and knew it was going to hard to hold him, with his super strength. Eventually Natasha nodded and went over to stand across from Bruce, Steve following close behind her. 

"How do I get this suit off?" Bruce asked. Peter reached up and weakly pressed the spider on his chest and the suit loosened. "Oh, thank you Peter." Bruce replied.

Unfortunately without the suit adding pressure to his arm, there was another rush of blood. "Wow, really not good." Bruce pulled the suit away so his arms and chest were bare. " Natasha, hold his other arm and chest. Steve holds his stomach and legs. Peter, this is going to hurt, I'm sorry." 

~~~~~~~~~~~~

About halfway through the surgery, Peter had passed out from pain. Natasha and Steve still held onto him though, in case he woke up for some reason. After Bruce was done, he sent Natasha to search Tony's lab for the special blood he had made in case Peter ever needed a blood transfusion. After half an hour of searching they finally found it and hooked Peter up. 

The question still remained though,

Where was Tony? 

~~~~~~~~~~~~


	6. Chapter 6

Peter slowly blinked his eyes open, but quickly shut them groaning, the bright lights hurting his eyes. Natasha, who was sitting next to his bed noticed, "Peter? Bud, are you awake?"

"Friday," he mumbled, "dim the lights." Friday complied and Peter opened his eyes, looking over a Natasha. He surveyed the med bay, "What, wh-why am I here?"

Natasha furrowed her brow, "Do you not remember? You landed on the balcony around 1 a.m. last night. You're arm was badly bleeding and so we brought you here to stitch it."

"But why are you sitting with me?" Peter asked, confused, "Where's Ton-oh." Peter looked away, blinking back tears, "I remember now." He replied hoarsely.

"What happened Peter? If you tell us we might be able to help." Natasha placed a hand on Peter's shoulder and he looked back at her.

"C-can we go to the living room to talk?" He questioned.

"Of course," Natasha handed him a folded pair of jeans and a science pun t-shirt. "You know the way there, I'll leave you to get changed." As she left, Friday slid a white privacy covering over the glass.

~~~~~~~~~~~~

Not even ten minutes later, the elevator dinged and Peter stepped out. Natasha, Steve, Bruce, and Rhodey who had all been staying at the tower were sitting on the couches. Peter went and sat in chair across from them. "Hi." he said.

"What happened last night?" Rhodey asked, skipping right to the point.

Peter sighed before recounting everything that had happened from when Evil Dude attacked them until he landed on the balcony. He glanced over at the glass door and was relieved to see there were no bloody handprints anymore. 

Everyone was silent.

Eventually Steve spoke up, "We have to find him."

"Yeah, no kidding. But how?" Rhodey replied. 

"Can we track his suit?" Bruce inquired?

Peter shook his head, "The EMP he was hit with would have fried the wiring. And if they're smart, which they are since they were able to capture Iron Man, they would have removed the tracker. We could try tracking the implant in his arm, but that one might be destroyed as well. Other than that I don't know of any other GPS devices he has."

For a long while everyone just stared at the floor, their hands, or out the window. "Oh my gosh..." Natasha said quietly. Everyone looked at her, "Who's going to tell Pepper?"

"Do we have to? Can't we just wait till we have a lead on Tony or something?" Bruce asked.

"Of course we have to tell her. Who knows how long it will take to get a clue on Tony's location." lectured Rhodey, "Besides, you know Pepper, if we don't tell her she'll figure it out. Then she's going to be sad and angry."

"I can do it," Steve said standing. 

Peter nodded, "Thank you Mr. Steve."

~~~~~~~~~~~~

As it was, Pepper was still angry on top of being heartbroken. But she wasn't angry at any of the Avengers. Her fury was directed at the despicable humans who had the nerve to kidnap her husband. That evening when she was finished with meetings for the day, she rode the elevator up to the living room area. When Pepper stepped out, she saw Steve and Natasha cooking dinner and Peter, Bruce, and Rhodey staring intently at computers, seated around the dining table. Steve looked over at her, "Hello Miss Potts."

"Hey Steve, any leads so far?" She inquired, looking over everyone.

"Possibly..." Peter muttered, "The last known location of Tony is the middle of 53rd street. After that, wherever they put him, the walls are either blocking the signal or the tracker was destroyed. I'm guessing both."

Pepper stood behind Peter, looking at his computer screen. "Were there any security cameras that would have seen the vehicle or it's license plate."

"Yes there were." Peter replied glumly, "Unfortunately the vehicle didn't have any license plates and the car was a black Toyota Rav 4, one of the most popular cars in New York. There's literally hundreds of thousands of them registered here."

"Facial recognition from the cameras?" Pepper tried desperately.

Rhodey shook his head, "Tinted windows and masks. These guys are real professionals."

Pepper sighed in defeat and took a seat next to Peter. "This isn't going to be easy." 

~~~~~~~~~~~~


	7. Chapter 7

Every day.

Again and again and again.

Same routine. Same time.

But what they used differed a little bit each day. 

Sometimes after being drug to his cell and passing out from exhaustion, he'd wake up to find burns. Other days it would be cuts and gashes all over his skin. Sometimes it would just be bruises, lots and lots of bruises. When that happened he would often cough up blood for a while after that. Occasionally he woke up cold and clammy and assumed they had either electrocuted him or used drugs of some sort. Possibly both.

While they tortured him, they'd always ask questions. He could barely hear them, much less comprehend or remember them, over the rush of blood in his ears and a pounding headache. He tried to answer as few as possible. But sometimes the pain was too much and he'd finally break. He hated himself when he gave them what they wanted.

He kept getting weaker and weaker each day. The one meal a day didn't do anything to help that. But it wasn't just physical weakness, he was emotionally and mentally exhausted. 

All Tony could think was hurry.

Please hurry.

~~~~~~~~~~~~


	8. Chapter 8

had been two weeks since Tony disappeared. The Avengers were no closer to locating him. They had searched 53rd street where his tracker signal had gone silent and the surrounding three square miles.

Peter was beginning to lose hope, he couldn't think of anything else to try.  
He had begun to talk Friday often. Don't misunderstand, he still loved his AI, Karen, but Friday was Tony's creation. And well, it was somehow comforting. 

Peter laid in his bed Saturday morning, throwing a ball at the wall. It was unusually quiet in the Tower, since Pepper was at work and the other Avengers that were staying there had gone to S.H.I.E.L.D. for some meeting. Peter sighed, "We're sure we tried using all the trackers located on Tony to find him, right Fri?"

"Every one in my knowledge." Friday confirmed, "However, I could try searching some of Boss's oldest databases that he didn't bother installing into my memory for any others if you'd like."

"Of course Friday!" Peter jumped up from his bed and began to pace, "You should've mentioned that sooner. Alert me with your results."

Peter waited about 20 minutes, this was taking longer than he'd expected. He figured Friday could tell him what she found wherever he went in the Tower, so he prepared himself a snack in the kitchen. 

He had just sat down with his food when Fridays voice rang through the speakers, "Mini Boss, I think I may have found something."

Peter's eyes widened as he perked up and placed his plate on the coffee table, "Tell me."

"In Boss's old files I found a record from 2009 that says he implanted a tracker at the base of his neck on the right side. I hacked into it, and though outdated, it still appears to be working."

"Fri, a-are you saying we know where Tony's at?" He almost didn't want hope, this was too good to be true.

"I believe so, yes."

Peter leapt from the couch and started heading to his room. "Send the coordinates to my suit Friday."

"Which suit, Mini Boss?" She questioned.

Peter stopped and thought about it for awhile before deciding. "Stealth suit would probably be best..." He muttered before saying to Friday, "Send location and map to the Night Monkey suit."

"Right away."

~~~~~~~~~~~~

Peter was changed and swinging to his destination in record time. It was for the better as the location was 40 minutes away and there was absolutely no time to waste.

When he finally arrived, Spiderman perched in a tree near the building. It seemed to be a shipping warehouse of some sort. "Karen, can you pull up the schematics of the building for me?"

A map appeared before him in a small hand held projector. It was a complicated layout of rooms and hallways, stairwells and vents. "Wo," he mumbled, "this isn't confusing at all." 

*Please note sarcasm*

"Would you like me to separate each floor?" Karen asked

"Yes please." Each of the floors divided and the first one appeared before him. "Karen, how large are those air vents?"

"The primary ones which connect to most of the rooms are 2ft × 2ft."

"That's large enough for me to fit inside! Karen, scan for life and tell me which floors and rooms they are located in."

"Scanning... Here you are." There appeared to be three people roaming the halls, five or six on the main floor all in the same room, and a single person in a basement room. 

"What type of rooms are on the basement level?" He asked as the details appeared before him. Karen told him about all the different rooms, furnace rooms, electrical rooms, etc. but only a few caught his eye. The four, empty concrete ones and a larger room filled with laboratory and experimentation equipment. "Using the ventilation system, plan a route that avoids the most people but takes me to the person in the basement." Peter shut off the projection and slipped it into a pocket. The map he asked for appeared in mini form inside his mask. "Alright," Peter said,

"Let's go rescue Iron Man." 

~~~~~~~~~~~~


	9. Chapter 9

Peter was thankful for his spider powers. He climbed the whole way on the roof of the vents, finding it was quieter. When he finally arrived at the basement room he peered through the grate. Sure enough, there was Mr. Stark, cuffed to a wooden chair. Peter breathed a sigh of relief, even though Tony looked terrible, he was still alive. "Okay," he whispered, "Karen, there's probably some sort of silent alarm that will go off if I try to enter from here, can you hack it."

"Yes Peter, I can. I will only keep the alarm system down for ten seconds however, so as not to cause suspicion. Though you may want to know, you have already triggered three silent alarms during your time in the building."

"What?! Why didn't you tell me about them Karen?" Peter whisper-shouted.

"You did not ask so I figured you already knew or didn't care."

"No no no this can't be happening. Ugh, always warn me whenever there is an alarm!"

"Will do. Would you still like me to hack into the system?"

"Yeah, and while you're at it, permanently shut down any cameras in the cell as well."

After a few minutes of anxious waiting, Karen spoke up, "Systems offline in 3...2...1. You have ten seconds to exit the vents."

Peter pushed against the grate and it popped off with ease, sticking to his fingers. He walked down the wall and set the grate down on the floor. Spiderman carefully made his way over to his mentor. "Mr. Stark." It took a few times of repeating his name before Tony woke up and stared at him. 

"Peter..." He said tiredly.

"Hey Mr. Stark," Peter flipped the eye mask up on his suit, so Tony could see his eyes. "It's going to be ok, I'm gonna get you out of here."

"Peter, it's...it's not safe here. You have to leave right...right now."

"Not without you Mr. Stark." Spiderman pulled out a lock pick from one of his few pockets and knelt before Tony, starting to work on the cuffs.

Eventually the cuffs were unlocked. It took a few minutes longer than anticipated since he had only picked locks once before. As soon as his hands were free Tony leaned forward and hugged Peter as tightly as he could, though it was still pretty weak. Peter gently hugged him back.

Their embrace was cut short by a commotion outside the room and the door being slammed open. Spiderman flipped his eye mask back down and stood protectively in front of Mr. Stark as three people flooded into the room. Two men and a woman by the looks of it, all heavily armed. Peter immediately started shooting webs at them, making sure they couldn't harm Tony.

All was going well and he was about to subdue the other male when the woman who had been biding her time in the corner pulled out a stun gun. She began firing. The first one missed him but the second one landed on his arm and Peter faltered. In that time the second man had stood up and wrapped a huge arm around Spiderman's neck. The third time the gun struck him dead center. After several more shots, Peter was out cold.

They secured Tony to the chair again and placed handcuffs on Peter before dragging him to separate cell and changing him into a white T-shirt and black sweatpants. The spider suit was left in the room, tracking beacon purposefully remaining intact. The woman pulled out her com and spoke, "This is Adrianne, we have the spider," she smiled coldly, "I repeat, we have the spider."

~~~~~~~~~~


	10. Chapter 10

Natasha arrived to the Tower earlier than the other Avengers, around 3 p.m. It was oddly quiet, she had expected Peter to be there. Natasha assumed he was out on patrol, and didn't think much into his absence. At least, not until the others began showing up around 6 p.m.

"Hey Natasha."

"Hey Steve. How were the extra meetings?" She asked with a smirk, glad she didn't have to stay for them.

Steve rolled his eyes, "Boring as usual. Is Peter here?"

Natasha frowned, "No, he was gone when I arrived, so I figured he was on patrol."

Steve sat next to her at the island. "Fri, how long has Peter been gone?"

"Peter has been gone since 9:12 a.m." Friday replied.

"Nine a.m.?" Natasha was shocked, "Friday call his suit." 

They waited.

And waited.

And waited.

Nothing.

Steve and Natasha shared a troubled glance. "You don't think..."

"That the same people who took Stark have Peter? Yeah, I do." finished Steve. Just then, the elevator dinged and Bruce and Rhodey stepped out. They stopped their conversation in mid sentence when they saw Steve and Nat's worried looks.

"What's wrong?" Rhodey asked as him and Bruce hurried over to the kitchen island.

"It's Peter." Natasha answered

"He's gone."

~~~~~~~~~~~~

"Wait what?" Bruce said.

"What do you mean, 'Peter's gone'?" Rhodey growled.

"I came home at 3, right? And he wasn't here so I thought he was being Spiderman. Until Steve came home and we asked Friday when Peter left and he's been gone since 9 a.m." Natasha explained shakily.

"It's ok Nat," Steve laid a hand on her shoulder and she nodded, "we'll find Peter, we'll find them both."

~~~~~~~~~~~~

Half an hour later the team was suited up and about to leave. Bruce was hanging back, in case they found Peter and Tony and needed medical attention. "Alright," Steve said, "let's go."

The three of them, Rhodey, Steve, and Natasha, left the tower. Rhodey was flying in war machine and Steve and Natasha were both driving motorcycles. They followed the map Friday gave them to the location of Peter's spider suit. 

It only took them twenty minutes to drive and fly to the warehouse, where they congregated outside. "Ok everyone, coms in. Natasha, you get to the suit's signal, Rhodey and me will make sure the building's clear."

Everyone hurried inside, careful to be quiet. Within 10 minutes Natasha spoke into her com.

"Steve?"

"Building's clear." He replied.

"I-I found the suit. Just the suit. It's crumpled in the corner of this basement room. Peter's not here." She said, her voice breaking slightly.

Steve sighed, "Grab it. We'll head back to the Tower. There's nothing here to indicate where they went."

The met together outside and quickly left. Since they didn't drive and fly as fast going home as they did on their way there, it took them a little under forty minutes. Rhodey, Natasha, and Steve all met in the living room, where Bruce was waiting, and told him what they found. 

After minutes of silence, Natasha stood, "I'm going to take a shower and clear my head. Bruce, why don't you order some food?" 

Everyone went their separate ways, leaving Bruce in the living room. 

Where had Peter and Tony gone?

~~~~~~~~~~~~


	11. Chapter 11

Peter groaned when he woke up and went to rub his eyes, when he realized he couldn't. His wrists, shoulders, ankles, legs, stomach, and forehead were all strapped to a cold, metal table. That was the first thing he realized. The second was that he was no longer in his spider suit. Peter looked around the room as best he could without being able to move his head. There were harsh fluorescent lights on white tiled ceiling. The walls were a light gray and the floor was... Well, he couldn't see the floor. The wall closest to his feet had a large window connected to a short hallway. He assumed it was so people could watch him without being in the same room.

Peter looked to his right and left. There were computer screens on each side along with two chairs. A few metal carts held all sorts of medical equipment and tools as well as needles.

Lots and lots of needles. Most filled with strange liquid while a few were strangely empty. 

Peter didn't have much time to himself, however. A man in a white lab coat walked into the hallway and looked at Peter through the glass. "You're up quicker than expected. Those drugs we gave you should've lasted longer." 

"Yeah, well my metabolism likes doing that." Peter's voice was scratchy and dry, and he was just now realizing how thirsty he was.

The man smirked, "You're metabolism, you say?" Peter's eyes widened at what he just disclosed. "Interesting," the man continued. "Very interesting. I will have to inform Boss." 

"And who might that be?" Peter quipped. The man said nothing and exited the hallway, a mad grin on his face. 

A door to his left banged open. Hallway man and another man and woman, both in lab coats, walked in. Peter looked at the man he recognized, "Hallway man. Back so soon?"

"It's Ulrik to you, idiot. And yes, Boss wants us to begin tests, surprising since he's not here yet, but understandable."

Peter sighed, "You still haven't told me who this Boss of yours is."

"In time, you will find out. I'm sure of it. Now, it's time to begin."

~~~~~~~~~~~~

Tony's body ached. Probably drugged again, he thought. Nothing new, it happened at least once every four days. What he assumed were days at least, he honestly had no idea how long he'd been gone.

He was again cuffed to a chair, but something felt... Different. They were definitely in a new prison. In front of him was a computer screen on top of a small metal table. He had a horrible hunch that his new torture would be having to watch whatever was showed on that screen.

And he was right, as it flicked on to show an image of Peter. He was stationed to a metal table while three people stood and sat around him. Various tools and needles and more computers were placed around him on tables and carts.

Whatever was about to happen wasn't going to be good.

~~~~~~~~~~~~

Peter stared at the ceiling, trying not to panic, as they placed some type of collar around his next. "This first part will be simple," Ulrik explained, "we will ask you a series of questions about your mutant abilities-"

"Superhero powers." Peter corrected. He instantly regretted it as an electrical current ran through his body. It wasn't powerful enough to kill him, but it hurt enough causing him to gasp in pain.

"Insubordination will not be tolerated. You will speak only when spoken to. Understand?"

Peter nodded and whispered out a short, "Yes."

"Good," the man went back to explaining the test. "We will ask you about your mutant abilities, and you will provide us with answers. If you do not, well, I bet you can guess what will happen."

Peter nodded again. If he didn't provide answers they would electrocute him...

Peter was electrocuted a lot. He refused to respond to their questions, knowing they would use the knowledge against him. Though he suspected they already knew some of what they were asking him. 

By the time they stopped asking questions, he was sweating and pale and he couldn't stop shaking. I hope Tony is ok, was still the only thing he could think when they were done with him, however. 

~~~~~~~~~~~~

Tony was not ok.

He had just been made to watch Peter be electrocuted over and over again for two hours straight. Not to mention listening Peter's cries of pain.

And Tony was helpless to stop it.

~~~~~~~~~~~~


	12. Chapter 12

Every waking hour of every day hurt. 

He had lost track of how many sensory overloads he was forced to endure as they tried to understand him. As they tested his limits. And since he couldn't very well sit in a pitch black, noise cancelling room, the agony would last for days. He would rarely be fully recovered before it would start over. 

They would cut and bruise him then observe his enhanced healing. But since they would only give him one measly meal a day, his healing wasn't doing so great, and he was losing a lot of weight because of his increased metabolism. The people weren't very happy with his healing's poor demonstration. He told them he needed more food for it to work better, but his 'insubordination' as they called it only led to him being shocked into silence.

Recently, they would take him to an arena of sorts for hours at a time and force him to battle men and women much larger, more agile, and stronger than him. He was pretty sure this more for spectacle as they should have known full well how weak he was. He barely managed to block the hits and kicks sent his way, much less fight back.

Today was different, thank goodness. Nothing happened to him except for the fact he received two meals. That was amazing. 

In his gut though, he knew that this special treatment was probably leading to something extremely bad.

And Peter was not looking forward to it.

~~~~~~~~~~~~

Tony watched it all. Whenever they would hurt Peter the computer would turn on and a loud buzzer would go off. It was annoying if he was awake, but when he was asleep he felt thankful that it woke him. He didn't know why, but if Tony didn't watch everything they did to Peter he felt ashamed. Look at what Peter is being forced to endure, and Tony can't even watch? Pathetic.

Tony hated this. Hated whoever had them. But what he hated most was he couldn't be there for Peter, and he couldn't get them out of this blasted prison.

~~~~~~~~~~~~

For only two days, Peter got sweet respite and two meals a day. Then the normal lab people came, whose names he learned were Ulrik and Gorgonio (he had also heard whispers that this place was called the raft, but he was pretty sure this prison wasn't a wooden boat).

Ulrik was holding a white plastic container with a lid and Gorgonio pushed a metal cart with a knife and medical tools. They didn't say anything to Peter, which was normal. He stared at them quizzically but they didn't even look at him. They made sure his inner left arm was exposed before more restraining straps were placed on his wrists. 

Ulrik grabbed one the knife and plunged it into Peter's radial artery near his wrist. Peter gasped in pain and scrunched his eyes closed. He felt a tube being shoved into the jagged hole. He opened his left eye just a little and saw blood flowing through the tube into the white container. 

"What, what are you doing?" He croaked. Surprisingly, he wasn't electrocuted. Unsurprisingly, they didn't answer. He just watched for who knows how long, as his crimson blood drained into the white basin. He watched, that is, until he saw black spots dance across his vision, before he fell unconscious.

~~~~~~~~~~~~


	13. Chapter 13

The team was devastated.

Within two weeks, they had lost both Peter and Tony. Since then another two had past.

No new leads had appeared, they hadn't expected any. Each night they'd sit around the couches in the living room, rarely talking, but thinking desperately of ways to find the two. Always to no avail. Pepper would only join them occasionally. She tried to keep extra busy with SI work, in an attempt to keep her mind off her missing husband and practically son. 

Finally tonight Rhodey spoke up, "This is pointless. We sit here every night trying to think of where Peter and Tony might be. Yet we're getting nowhere."

"What else can we do Rhodey? We've already exhausted every other possibility of where they could have been taken." Natasha replied solemnly.

Rhodey shrugged, "I don't suppose you know here Peter or Tony is, do you Fri?" He had meant it sarcastically and wasn't expecting a useful answer. So Rhodey was shocked when that's what he received.

"I do not know where they are. But I could try tracking Tony the way Peter did." She answered

"Friday, do you mean to tell us you might be able to find them, and you didn't tell us?" Steve questioned.

"You did not ask." Friday replied curtly.

"Remind me to have Tony fix you so that you tell us facts that deal with the life or death of our friends, without our having to ask." Rhodey commented.

"Reminder made." Rhodey rolled his eyes.

"Friday, how did Peter track Tony?" Natasha asked, getting back on subject.

"Peter asked me to use Tony's older tracker in his right arm. I did and then sent the location to Karen, his spider suit AI."

Rhodey was surprised, "I didn't even knew he had a second one. I'm surprised it still works with how outdated it probably is."

"Surprised but grateful. Friday, try doing the same thing." Steve ordered, "Let's just hope that wherever they are now, the signal can still reach us." 

They waited in silence for several agonizing minutes, before a map appeared before them, a red dot showing Tony's location. Everyone stared at it, dumbfounded. 

Bruce spoke up for the first time that night, "Why are they in the middle of the ocean?" 

At that moment the elevator doors opened and Pepper walked in, looking at her phone, "Who's in the middle of the ocean."

"Peter and Tony. Supposedly. That's where the location of Tony's tracker is, at least." Natasha explained.

Upon the mention of Tony's name, Pepper quickly looked up and hurried over to the couch, pocketing her phone. "What structure could be in the middle of the ocean?" She glanced at everyone.

"Nothing really-" Bruce started.

"Unless..." Steve interrupted. He looked to Natasha, "You remember that underwater prison that was made using shield funding?" 

Natasha's mouth went dry and she nodded. "You don't really think that's where they are do you?" When Steve didn't reply, Natasha knew the answer. "Oh gods... Friday," she said shakily, "the, the tracker. Is it's location coming from a building of any type?"

The map zoomed in closer to the beacon. "Yes, the signal is coming from a place known as 'The Raft'."

Everyone looked worried and upset at this news, except Bruce. He was confused. "The Raft? What's that?"

"It's a prison, specially designed to contain enhanced individuals. But I doubt they're just holding him there." Steve said grimly

Natasha nodded, "If whoever kidnapped Tony and Peter took them there, nothing good is happening. We have to find them, and fast."

~~~~~~~~~~~~


	14. Chapter 14

Everyday they would come into his room. Drain him of his blood.

He was fairly certainly he was unhealthily low on that stuff. He would usually pass out as they bandaged his arm together. He no longer even had the strength to cry out in pain, as they would take their knife and undo the little healing his body had managed. 

He knew he was dying. 

And he knew it would happen soon.

~~~~~~~~~~~~

His heart had been shredded.

Patched together, only to be ripped apart again.

The beatings had begun again, along with being forced to watch his kid suffer. 

His weak and exhausted sleep was plagued with nightmares of the torture. He often woke up in a cold sweat, and terrified.

Where are you guys? We need you.

Help us.

~~~~~~~~~~~~

"I'm coming with you." Pepper said firmly. The rest of the team, who were already on their way to there rooms, turned and looked at her. She stood and began walking towards Steve.

"Pepper, we can't let you. You'll just be another person we have to protect since you don't have any armor. And we can't afford that, not with Tony's and Peter's lives on the line." Steve explained.

Pepper just glared at him, "And how do you know that I don't have armor?"

Steve was a loss for words. He didn't know if she had armor, he just assumed she didn't. Guess I'm wrong, he mused.

"That's what I thought. A quinjet will be waiting on the roof in 15 minutes. Be there. Be ready." With that, Pepper stalked off to her room.

"You heard her. Be ready." Steve repeated. 

~~~~~~~~~~~~

Pepper arrived to her and Tony's room and shut the door. She slipped off her shoes and debated whether or not she should actually go. Pepper of course, had a suit, but with her recent health condition she wasn't sure if she should go. Stop, she told herself, you have to go, Tony needs you.

With renewed assurance, she hurried over to her walk-in closet. Pepper went to the back wall and pressed her hand to the wall. Instantly, the wall folded back to reveal her armor.

~~~~~~~~~~~~

After fifteen minutes everyone was loaded in the quinjet. Rhodey in his war machine armor, Steve with his shield, Natasha with her widow bites, and Pepper in her silver and purple Rescue armor. Bruce was along, but would stay on the jet for medical assistance. Over the next forty-five minutes, the team formed and discussed their plan. Rhodey would search for Peter and fly him back to the plane, and Pepper was to do the same with Tony. Steve and Nat we're going to secure the place. Aka kill anyone they found for hurting their precious father-son duo. 

Pepper paced the floor worriedly. She wasn't sure what they'd find, and that scared her. 

"Hey," a voice broke her out of her thoughts, "we'll find them, ok? They're going to be ok." 

Pepper turned to the source of the voice and saw Natasha. "I wish I could believe that."

~~~~~~~~~~~~

With stealth mode and a cloaking device on, they gently set the plane down. They were lucky that the prison was out of the water. Everyone snuck out of the jet and followed the routes discussed over a map. After four minutes, Natasha spoke over the coms, "Tony is being held on level 7 cell 25a. Peter is on level 4..." she faltered.

"What's wrong Natasha?" Steve questioned.

"Peter he's on level 4... experimentation room 12."

Silence.

No one spoke over the comms. All too horrified as to what could be going on in that room. 

Finally Rhodey broke the silence, "Come on, let's go break them out."

~~~~~~~~~~~~

Pepper was still hurrying towards Tony's cell when Rhodey voice crackled to life again, "Guys... I found him. It's, it's not good. Bruce you need to be ready with some blood and IVs, lots and lots of blood."

Pepper shivered at the thought of why the kid would need so much blood, but returned her mind to the mission at hand. Little time passed before she made it to the door and blasted the lock. She barged through and swiftly went over to Tony and broke off his restraints. Pepper's helmet retracted, "Tony."

"Hey Pep..." Tony stared at her with exhaustion. His eyes full of recent horrors he was forced to watch and endure. "Is it really you?"

Pepper smiled, tears in her eyes, "It's really me, baby." She placed a hand on his face and he grasped onto it like a lifeline. "You're safe now, but we have to leave."

"Peter..."

"Peter's fine, he safe." She reassured, "Rhodey found him and took him back to the quinjet. Right now let's focus you." 

Tony nodded and placed his hands on her shoulders. Pepper grasped his waist, knowing he probably couldn't stand on his own. And she was right. His knees instantly gave out and he would've fallen if Pepper hadn't caught him. She picked him up bridal style and began carrying him out. 

They only ran into 5 people. Nat and Steve had done their job well. Within minutes they were loading onto the quinjet, Tony having passed out. She laid him on one of the prearranged medical cots. Peppers suit retracted off her and folded down into a cube. She looked over and saw Peter and gasped. "Oh my gods. What happened?"

He was painfully skinny and pale his forearms skin was torn and mangled. They had taken off his shirt and Pepper saw many scars and bruises and even a few burns. They had already hooked up lots of IVs to him. "Let's just say, a lot of stuff." Bruce said.

Pepper breathed shakily and sat down next to Tony's bed, holding his hand. Natasha and Steve rushed in, "Let's leave before the rest of our 'friends' show up." Natasha ordered as she made her way to the cockpit. She sat down next to the pilot, who was a shield agent, and the jet took off. 

Not even ten minutes into the ride Pepper mumbled something about motion sickness and stumbled into the bathroom. Natasha turned to Bruce, "Is it just me, or has she been acting... Different?"

~~~~~~~~~~~~


	15. Chapter 15

Three whole days.

That's how long it took before Tony woke up. His eyes fluttered open, and he was very confused. He looked around the room before seeing Pepper sitting in a chair beside his bed. "Pepper?" He asked tentatively.

Pepper quickly looked up, putting away her phone. "Tony," she smiled, "oh my gosh you're awake."

"Where am I? Wh-what happened?" He stuttered.

"Three days ago," she explained, "we found where you were being held. We came as fast as we could and rescued you. Since we got back the Tower, you and Peter have been recovering in here."

His eyes widened at Peter's mention. "Peter... Wh-where? Is he ok?" Tony's eyes darted around the room, looking for his kid.

Pepper moved her chair closer to his legs so he could see Peter in the next bed over. Peter was still pale and scrawny, he had multiple IVs hooked up and bandages covered his skin. Tony immediately sat upright, too fast as it made him dizzy, giving him a headache. He tried to swing his legs over the edge of the bed and go to Peter but Pepper stopped him. "No. Tony, what do you think you're doing?"

"Pep, I have to go to him. I need to be with him." He tried desperately.

Pepper fought back, as she pushed his legs onto the bed, "You can be with him on your bed. You are still too weak to stand. It would be better for Peter if you heal, so you can give him proper care. Please Tony." Her eyes softened and in them he could see all the emotional pain and stress she had been forced through in the past days. Weeks? Months? He wasn't sure, so he asked.

"How long were we gone?"

Pepper looked at her hands as a tear ran down her cheek. "Four weeks," she whispered hoarsely, "a whole month."

He leaned forward and gently wrapped her in a hug. She folded her arms around his waist in return. "It was so hard while you were gone Tony," she cried, "with all the stress of work and the press. You don't know how many times I cried myself to sleep, wishing you were by my side."

Tony was trying, and failing miserably, to keep his tears in too. "I'm so sorry Pepper. I never wanted this to happen. I didn't want to put you through this again." He kissed the side of her neck, and held her closer.

"I'm so glad you're back. Please, never leave me."

"I won't my dear, never again." Tony unfolded from the embrace and pressed his forehead to hers, as he rubbed her shoulders.

How long they stayed like that, Tony wasn't sure. But he did know, he never wanted it to end.

~~~~~~~~~~~~


	16. Chapter 16

A week later, Tony had recovered well. He was even able to walk without anyone helping him; though scars remained as torturous reminders of what they had been forced through. 

He refused to leave Peter's side, even at night. He knew Pepper didn't like it much, but he had to be there when he woke up. He was lucky enough that his amazing wife would bring him food, otherwise he probably wouldn't eat. 

It was around eleven at night, Tony was dozing off in his chair beside Peter. The kids eyes flew open, and he looked around panicked. In his arms were many needles, increasing his freak out. He started rapidly ripping them from his skin. Within seconds they were out of him and he was kicking the thin sheet off his legs. By now Tony was fully awake and moving to stop Peter. Peter swung his legs over the bed and tried to stand, but instantly fell as his knees gave out. Thankfully for him Tony was by his side and caught him. "Peter! Peter calm down it's ok, we're safe."

Peter looked at him, eyes wild with fear. "Kid, you're safe you're with me. We're at the Tower." Tony guided him back to the bed and they sat. "How do you feel?"

"Terrible. Weak. Scared." Peter replied quietly.

Tony sighed wrapping Peter in a hug, "I know kid, I know. I'm so so sorry this happened. I won't ever let anyone get you again." 

Peter nodded into Tony's shoulder and held onto him tightly as he started to cry. "It hurt," he sobbed, "it hurt."

Tony just rubbed his back, knowing it was better to let Peter talk and cry. 

A while later, Peter finally stopped crying and pulled away from the hug. "Thank you... I'm sorry. This is really stupid."

Tony stared at him incredulous, "No kid, this isn't stupid. And you don't have to be sorry. You didn't ask for what they did to you. And I know what happened, they had this screen, I watched it all."

"Then you saw how weak I really am." Peter said.

Tony gave him a stern, yet kind, look, "Peter. Listen closely. You are so amazingly strong and brave to endure all that pain and come out of it alive. I don't know anyone as strong as you kid."

After minutes of silence, Peter finally talked, "Can we get some food?"

Tony chuckled, "Of course we can."

~~~~~~~~~~~~

Tony helped Peter walk to the elevator and then to the couch. Once Peter sat down and had a blanket around him Tony asked what he wanted to eat. "Can I have chicken nuggets and french fries."

Tony laughed again, smiling, "Of course you can, I'll put them in the oven."

Fifteen noisy minutes later, Tony finally came back. "I don't think anyone makes as much noise in the kitchen as you."

Tony ruffled the kids hair, "Gee thanks, kid."

"Tony?" A voice called, coming closer, "What are you doing?" Pepper walked out of the hall, wearing pajamas. 

"I'm making chicken nuggets." Tony replied simply.

"Why?" She asked.

"For me." Pepper turned and saw Peter, "Oh my gosh, Peter, how are you?" She rushed over and gave him a hug before brushing the hair from his eyes.

"I'm better then when I first woke up," he smiled and glanced at Tony who sat down beside him.

"Well that's good." She looked at Tony, "I think I'll leave you two be. Don't stay up too late ok?"

"Ok, Mrs. Stark." Peter responded.

"Peter, please, call me Pepper."

Peter blushed, "S-sorry Pepper." She smiled and gave him one more hug before heading to bed. 

~~~~~~~~~~~~

It was about two hours into their Star Wars marathon when Peter fell asleep, he was leaning on Tony's chest, who had his arm around Peter's shoulders. Tony had also fallen asleep when the kid began to twitch and jerk. He started mumbling incoherent words. It just kept getting worse and worse till he woke up in a cold sweat, tears streaming from his face. Peter was shaking horribly, and the room spun before his eyes. His breathing was jagged, and he could hear his heart rapidly beating in his chest.

"Peter? Peter!" The voice sounded distant and muffled. "Peter can you hear me?" A hand gently grabbed his face and turned it towards the voice. He saw Tony, a slightly blurry, Tony. "Kid look at me focus on me ok?" Tony grabbed Peter's hand and held it to his chest, "You need to breathe, copy me." Tony took really exaggerated breaths until Peter's finally became even. The world stopped spinning and Peter looked down."I-I'm sorry. It was just a stupid nightmare. I'm sorry-"

"Stop apologizing, Peter. It's ok. I have nightmares and panic attacks a lot. Nothing to be ashamed of." Tony was surprised to hear himself admitting that to the kid. Nobody but Pepper knew about it. "I'm so sorry you have to go through this Peter-"

"Don't. If I can't apologize neither can you, especially since this wasn't your fault, you couldn't have prevented it." Peter looked Tony in the eyes, he could see the man struggling to believe his words. But finally he gave in. 

"Fine, ok. Well it's 5 a.m. no point trying to sleep when we'll wake up soon anyways. Want to go to the lab? Upgrade your suit?" Tony offered.

"Sure..." Peter replied warily, "But is it possible to just like, build a robot or something? I need to take a short break from the superhero life." 

Tony chuckled, "Of course, I know what you mean."

~~~~~~~~~~~~


	17. Chapter 17

The whole week after Peter woke up was a nightmare. He was plagued with nightmares every night, usually unable to sleep after them, and multiple panic attacks each day. Peter was just glad that his da-Tony hadn't made him go back to school that week.

On Saturday morning, he was walking down the hall when his super hearing picked up in a conversation in Tony and Pepper's room.

"He needs help. The poor kid has nightmares and panic attacks all the time. He barely gets 3 hours of sleep every night, it's unhealthy." Pepper lectured.

"I know Pep, but what if he's uncomfortable with it? I don't want him to shut down because we mention it." Argued Tony.

"I don't care. If this continues he's never going to be able to live a normal life. Well, as normal as life can be for a spider kid." Pepper countered.

There was a beat of silence, "Fine. But who will we use? I don't want to send my kid to someone I don't trust." Peter's heart fluttered and he blushed slightly, does Tony really think of me as his kid?

"We can use the woman that you did after the Mandarin attack. She did amazing with you and I'm sure she'll do just as good with Peter. Besides, I've heard she's moved her business here." Offered Pepper.

"Ok," Tony sighed, "I'll see if I can make an appointment for Monday. When should we tell him?"

Peter opened the bedroom door, startling Pepper, "You don't have to tell me anything. I heard enough of it... What are-what are you going to do with me?"

Tony walked up and placed a hand on Peter's shoulder, "We setting you up with a counselor."

Peter's eyes widened, "Like a 'tell me about your problems and I'll help you deal with them' counselor?"

"That's the one," Tony confirmed.

"Peter," Pepper said from her seat on the bed, "We want you to be able to have-"

"a normal spider kid life?" Peter finished. 

"Y'know, we really need to work on this eavesdropping thing of yours." Tony commented.

Peter blushed deeply, "S-sorry, it's just hard not to with my enhanced hearing."

Tony chuckled and ruffled the kids hair, "I'm just kidding with you, Pete." 

Peter turned and started for the door but abruptly stopped, "Did you mean what you said about me being your kid?" He asked Tony. 

Tony's eyes widened, "Of course I did, Underoos."

Peter smiled and nodded, before heading for the door. A little extra pep in his step.

~~~~~~~~~~~~

Monday.

Peter was extremely nervous.

He had no idea what to expect. Would she ask him questions or was he to just tell her? What should he tell her? Should he tell her about Spiderman? All these and many more ran through his head, increasing his inner panic.

And he hadn't even gotten out of bed, though it was already 9:34. 

He was skipping school again today, since the only appointment time that was open was at 11 a.m. the middle of the school day. He heard a knock on his door, "Pete? Bud, it's time to wake up." His door opened a crack and light flooded in, Tony walked over to him and sat on the bed. 

"Tony, I don't feel so good. I don't wanna go today. What if I mess up and say something wrong? What if I tell her I'm Spiderman? What if-"

"Woah kid. Calm down, it'll be ok. Your first time there is usually pretty easy, so don't worry. And if you reveal you're Spiderman... I'll make her sign a paper or something."

Peter nodded and sat up, leaning in to give tony a hug. "Thank you." 

~~~~~~~~~~~~

Peter's first appointment went well, just like Tony said it would. He really liked the woman he worked with, as she was really nice. Not all the sessions were as bright and peachy as the first, though some were. Others he would come out quiet and grumpy, not wanting to talk to anyone and just work in the lab. And them there were those sessions. The ones he would stumble out of, weak and eyes bloodshot from crying. That's why Tony made sure he was always there early to pick him up. And why Happy always drove, in case Tony needed to be with Peter. 

Whenever those appointmemts happened, Tony would always hurry to Peter's side, and help him into the car. He would hug him when he started to cry again, whispering reassuring words in his ears. As soon as they would arrive home, Tony would help Peter to the couch and grab them both a container of their favorite ice cream to eat while watching movies. When Peter was finished eating he would lay down, resting his head on Tony's lap, while Tony ran his fingers through Peter's curls. He wasn't sure why, but it always seemed to calm and comfort the kid.

Today all this happened again. Peter was about to fall asleep, but before he did, he mumbled, "Thanks, dad."

Tony's heart did flips inside his chest, and he smiled like a little child. This kid, his kid, just called him dad, and Tony couldn't think of a happier moment in his life. "Anything for you son." He replied quietly.

~~~~~~~~~~~~


	18. Chapter 18

A few days later Tony was laying in bed waiting for Pepper. Since the kidnapping, he had been making a point to sleep with his wife instead of work in the lab. He knew she appreciated it. Tony had been noticing something was different with her, but he was unable to place it. He watched her movements as she came out of the bathroom and laid down next to him. "Hey." She said with a smile.

Tony returned the look, "Hey. Have, have you been feeling ok? Something's different about you."

Pepper looked a little taken aback, "Yeah, I'm fine. But, I was wondering if we could have a date tomorrow night? I had wanted to have one a month ago, but well, you know..."

Tony placed a gentle kiss on her forehead, "I think that's a wonderful idea. Should I make a reservation somewhere?"

"No, no. I have it covered." She assured him.

"Ok, sounds good Pep. I love you." He turned off his bedside light and she did the same.

"I love you too, goodnight." She replied.

"Goodnight, love."

~~~~~~~~~~~~

The next night, at 6:53 p.m. Tony looked in the mirror. He finished combing his hair and smoothed the wrinkles on his clothes. He wore a soft, dark blue t-shirt, a black blazer with black dress pants. Once he was satisfied with how he looked, Tony headed to the elevator. Pepper had told him to meet her on the roof for the date. He wasn't sure why, but decided not to question it. 

When the elevator doors opened and he walked out, the sight was beautiful. In the center was a large wooden pergola, with a wooden floor beneath. There were white drapes on top of the pergola intertwined with orange Christmas lights, which were also hanging off the side. In the far left corner were two plush leather chairs, with a dark wooden table in-between them. On it was a white candle and bud vase holding a single red rose. Pepper stood from one of the chairs. She wore a simple chunky knit white sweater, perfect for the crisp October air, and black slacks. She had on natural makeup and her hair held gentle curls.

In Tony's eyes, she had never looked more beautiful.

Tony smiled and walked up to her, "Hello beautiful."

"Hello dear." Pepper wrapped her arms around his neck. In return Tony hugged her waist and kissed her. 

When they finally pulled apart, Tony just stared into her eyes, "It's almost as beautiful as you up here."

Pepper laughed, "Well then I must have done a good job."

"You always do. Should we eat?" He asked.

"Of course," Pepper sat down in her chair, and Tony pushed it in for her, before sitting in his own chair. Each plate was already served with lasagna, and cooked, sugarglazed carrots. They ate and talked.

And talked, and talked for hours. Uninterrupted. It was amazing.

Eventually Pepper grabbed his hand and stood. "Will you dance with me?"

"Every day I would." He pulled her to the middle of the dance floor as music started to play. He placed his hands and on her waist and she placed her hands around his neck. They danced to songs like "Perfect" by Ed Sheeran, "When We're Together" by Mark Harris, "Chasing Cars" by Sleeping At Last, and many many more.

Never talking, except for the occasional 'I love you's'. They simply danced.

Finally Pepper stopped moving and looked at him. "Tony, I need to tell you something."

He gazed at her, but her expression was unreadable, which worried him. "What is it?" His tone slightly worried. But then she smiled.

"I... You... We're..." Pepper took a breath, "I'm pregnant."

Tony's jaw dropped, and he stood there shocked. "What? How long?" He finally managed. 

Pepper smiled widely, "About two months. I had planned to tell you a month ago, like I told you last night. But, well, life happened."

Tony cracked a smile, "Life sure gets in the way sometimes... I can't believe this Pep."

"I know, we're a family now. You're going to be a dad Tony, and you will be amazing. I know it." Tony's face had fallen slightly when she mentioned him being a dad. Pepper knew he was thinking of his dad, and worrying that he'd end up like that. "Don't worry Anthony."

Tony nodded, smiling once again, "I'm going to be dad. Oh my gosh, this is, this is more than I could ever ask for." He kissed her once again that night, holding her close, before bending down and kissing her baby bump, making her giggle. When Tony stood, Pepper didn't think she had ever seen such joy and happiness on his face. "Will that be all Mrs. Stark." He asked earning a small laugh as she remembered some of the earliest moments of their 'not quite a relationship yet' relationship. 

"That will be all, Mr. Stark." 

Tony put an arm around her waist as they walked into the elevator and to their bedroom.

Today was the best day of his life. He was going to be the dad of the love of his life's child. And he couldn't wait.

~~~~~~~~~~~~

**Notes for the Chapter:**

> That's the book y'all! There is a sequel that I will hopefully be posting soon.


End file.
